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*`OxyPOM` simulates oxygen consumption and production in river based on [Holzwarth and Wirtz, 2018](https://doi.org/10.1016/j.ecss.2018.01.020), including key biogeochemical processes as photosynthesis, respiration, mineralization, and nitrification.
-`OxyPOM` simulates oxygen consumption and production in river based on [Holzwarth and Wirtz, 2018](https://doi.org/10.1016/j.ecss.2018.01.020), including key biogeochemical processes as photosynthesis, respiration, mineralization, and nitrification.
*`DiaMO` is a simplification of `OxyPOM` and calculates oxygen consumption and production using a statistical inspired model.
-`DiaMO` is a simplification of `OxyPOM` and calculates oxygen consumption and production using a statistical inspired model.
The code of these models is located in the directory `./src` (e.g., `./src/oxypom` and `./src/diamo`), and future code developed as part of this model should be here included.
Together with `OxyPOM` and `DiaMO`, this repository includes the model `oxypom/light`: a second order correction for the calculation of photosynthetically active radiation depth profiles.
## Requirements
* This model requires:
-`FABM` (v1 or above) available in [fabm github](https://github.com/fabm-model/fabm/).
It can be cloned using `git clone https://github.com/fabm-model/fabm.git fabm`.
- This model requires:
* The physical driver:
-`GOTM` (v6.0 latest stable release) available in [gotm github](https://github.com/orgs/gotm-model/repositories).
It can be cloned using via `git clone --recursive https://github.com/gotm-model/code.git -b v6.0 gotm6`.
- `FABM` (v1 or above) available in [fabm github](https://github.com/fabm-model/fabm/).
It can be cloned using `git clone https://github.com/fabm-model/fabm.git fabm`.
- The physical driver:
-`GOTM` (v6.0 latest stable release) available in [gotm github](https://github.com/orgs/gotm-model/repositories).
It can be cloned using via `git clone --recursive https://github.com/gotm-model/code.git -b v6.0 gotm6`.
The following is not required to build and run the model but it is for running the test case:
* The script for downloading forcing and validation data requires the following shell commands:
-`wget`
-`unzip`
-`sed`
- The script for downloading forcing and validation data requires the following shell commands:
- `wget`
- `unzip`
- `sed`
* The scripts for generating forcing files setup and plotting routines for model validation require:
-`R` (v4.3 or above) available in [r home](https://www.r-project.org/) with the library `ncdf4` installed.
- The scripts for generating forcing files setup and plotting routines for model validation require: -`R` (v4.3 or above) available in [r home](https://www.r-project.org/) with the library `ncdf4` installed.
## Testcases
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@@ -70,10 +67,7 @@ This setup uses the physical driver `GOTM` to simulate the water column dynamics
1. To run the testcase go to the directory `.\testcases`.
The model is build with the script `gotm-installation.sh`, in where these variables must be defined:
-`GOTM_DIR` base directory of GOTM source code
-`FABM_DIR` base directory of FABM source code
-`OXYPOM_DIR` base directory of OxyPOM source code
The model is build with the script `gotm-installation.sh`, in where these variables must be defined: - `GOTM_DIR` base directory of GOTM source code - `FABM_DIR` base directory of FABM source code - `OXYPOM_DIR` base directory of OxyPOM source code
By default they are:
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@@ -84,10 +78,10 @@ By default they are:
```
2. The script `gotm-installation.sh` creates the directory `.\build` with the building files, and a copy of `gotm` executable in the `.\estuary` directory.
Now move to the directory `.\estuary`.
Now move to the directory `.\estuary`.
3. The script `get_data.sh` download and unzip the forcing and validation data from [kuestendaten.de](https://www.kuestendaten.de) in a newly created directory `.\data`.
The downloaded files are used under license [DL-DE->Zero-2.0](https://www.govdata.de/dl-de/zero-2-0).
The downloaded files are used under license [DL-DE->Zero-2.0](https://www.govdata.de/dl-de/zero-2-0).
4. The script `setup_data.R` formatted the data to be read by `GOTM`. It generates the file `meteofile.csv`.
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@@ -108,7 +102,7 @@ Follow steps 1-2 of the estuary testcase.
Now move to the directory `.\light`.
* The script `model_comparison.R` analyses the model output.
- The script `model_comparison.R` analyses the model output.
If everything is correct, the figure `light_validation.png` should be produced.
It displays a comparison of simulations using the default light implementation with the provided by `oxypom/light`.
